Gut Virome Case-Control Study in Colombia
27 fecal samples from Colombia in a case-control study of the gut virome in ICU and non-ICU hospitalized patients with diarrhea versus non-diarrheic individuals. machine-written summary
27 samples · 35 runs · CO · Age unknown · 2025 · 7.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 108 sample values (collection date, country, health condition, health condition detail) |
| ✓ Abstract / description | 27 sample values (location region) |
| ○ Full text | read; no usable statement or table · PMC12927239 |
| ✓ Supplementary tables | 81 sample values (age, sex, subject id) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 23 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 27 | 100% | ||||
| country | 27 | 100% | 27 | |||
| health_condition | 27 | 100% | 27 | |||
| subject_id | 27 | 100% | 27 | |||
| age_at_collection_days | 27 | 100% | 27 | |||
| collection_date | 27 | 100% | 27 | |||
| detailed_location | 27 | 100% | ||||
| health_condition_detail | 27 | 100% | 27 | |||
| location_region | 27 | 100% | 27 | |||
| sex | 27 | 100% | 27 |
- Metagenomic analysis of the human gut virome reveals functional signatures and viral stability across hospitalized and non-hospitalized diarrheal and non-diarrheal individuals. 2026 PMID 41725012 PMC12927239 own_data
Archive description
Background The human gut virome is a fundamental yet understudied component of the intestinal microbiome. However, its taxonomic composition and functional potential in Latin American populations remain poorly understood, particularly under clinical stressors such as hospitalization and diarrhea conditions often linked to microbial dysbiosis Methods We conducted a hybrid metagenomic analysis of the human gut virome from 37 fecal samples: 10 from patients admitted to intensive care units (ICU), 13 from hospitalized patients outside the ICU (Non-ICU), and 14 from non-diarrheic individuals, including taxonomic and functional profiling of viruses and detection of viral auxiliary metabolic genes (vAMGs). Results We identified 494 high-quality viral vOTUs, from which 37,619 ORFs were predicted. Taxonomically, Caudoviricetes and Intestiviridae were consistently present across all groups, supporting their role as part of a conserved core virome. Functionally, non-diarrheic individuals harbored more viral metabolic auxiliary genes (vAMGs) related to genetic recombination, suggesting a greater prevalence of temperate phages. We also identified resistance-related vAMGs, including ATP-dependent bacitracin transporters and Zinc D-Ala-D-Ala carboxypeptidase, highlighting the potential of phages as mobile reservoirs of antibiotic resistance. Conclusion Altogether, our findings reveal the coexistence of lytic and lysogenic strategies in the gut virome, shaped by clinical context. Our study provides evidence for the ecological resilience of the human gut virome and underscores the need to integrate viral communities into resistome research.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.title · “Human Gut Virome”
- host run.scientific_name · “Homo sapiens”
- body site study.description · “37 fecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA118914512 | age_at_collection_days | 14245.0 | R2 | 0.85 | paper.supp.13099_2026_811_MOESM5_ESM.xlsx[Samples!Age] | U01 | 39 |
| SAMEA118914512 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMEA118914512 | country | CO | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Colombia |
| SAMEA118914512 | health_condition | gi_infection_or_diarrhoea | R1 | 0.70 | sample.name_rule:sample_alias | U01 |
| SAMEA118914512 | health_condition_detail | U01 | R1 | 0.70 | sample.name_rule:sample_alias | U01 |
| SAMEA118914512 | location_region | Latin America | R4 | 0.10 | ena.study_description | poorly understood, particularly under clinical stressors |
| SAMEA118914512 | sex | male | R2 | 0.85 | paper.supp.13099_2026_811_MOESM5_ESM.xlsx[Samples!Sex] | U01 | Male |
| SAMEA118914512 | subject_id | PMetmed_01 | R2 | 0.85 | paper.supp.13099_2026_811_MOESM5_ESM.xlsx[Samples!Patient_ID] | U01 | PMetmed_01 |
Sequencing
35 runs over 27 samples · mean 4.73 Gbp per run (median 4.40 Gbp, total 165.60 Gbp; 35 runs with a base count) · layout PAIRED 23, SINGLE 12 · platform ILLUMINA 23, OXFORD_NANOPORE 12 · models Illumina NovaSeq 6000 (23), MinION (12) · 66% of runs with a Sandpiper profile · first public 2025-09-08 – 2026-02-02
Authors (0)
No author record.
Downloads
PRJEB95899.csv.gz (1.9 KB) · parquet (71.1 KB) — all 27 samples, every field with route and confidence · PRJEB95899_determinations.csv.gz (2.9 KB) — 216 evidence rows